Biology subjects

Verma, A.

Publications and source records attributed to Verma, A..

6 recordsLinked to original sources

bioRxiv2018

A robust nonlinear low-dimensional manifold for single cell RNA-seq data

Modern developments in single cell sequencing technologies enable broad insights into cellular state. Single cell RNA sequencing (scRNA-seq) can be used to explore cell types, states, and developmental trajectories to broaden understanding of cell heterogeneity in tissues and organs. Analysis of these sparse, high-dimensional experimental results requires dimension reduction. Several methods have been developed to estimate low-dimensional embeddings for filtered and normalized single cell data. However, methods have yet to be developed for unfiltered and unnormalized count data. We present a nonlinear latent variable model with robust, heavy-tailed error and adaptive kernel learning to estimate low-dimensional nonlinear structure in scRNA-seq data. Gene expression in a single cell is modeled as a noisy draw from a Gaussian process in high dimensions from low-dimensional latent positions. This model is called the Gaussian process latent variable model (GPLVM). We model residual errors with a heavy-tailed Students t-distribution to estimate a manifold that is robust to technical and biological noise. We compare our approach to common dimension reduction tools to highlight our models ability to enable important downstream tasks, including clustering and inferring cell developmental trajectories, on available experimental data. We show that our robust nonlinear manifold is well suited for raw, unfiltered gene counts from high throughput sequencing technologies for visualization and exploration of cell states.

genomics↗

bioRxiv2017

Occipital tACS bursts during a visual task impact ongoing neural oscillation power, coherence and LZW complexity

Little is known about the precise neural mechanisms by which tACS affects the human cortex. Current hypothesis suggest that transcranial current stimulation (tCS) can directly enhance ongoing brain oscillations and induce long - lasting effects through the activation of synaptic plasticity mechanisms [1]. Entrainment has been demonstrated in in - vitro studies, but its presence in non-invasive human studies is still under debate [2,3]. Here, we aim to investigate the immediate and short-term effects of tACS bursts on the occipital cortex of participants engaged in a change - of - speed detection task, a task that has previously reported to have a clear physiology - behavior relationship, where trials with faster responses also have increased power in {gamma} - oscillations (50 - 80 Hz) [4]. The dominant brain oscillations related to the visual task are modulated using multichannel tACS at 10 and 70 Hz within occipital cortex. We found that tACS stimulation at 10 Hz (tACS 10) enhanced both (8 - 13 Hz) and {gamma} oscillations, in hand with an increase in reaction time (RT) in the change - of - speed detection visual task. On the other hand, tACS at 70Hz desynchronized visual cortices, impairing both phase - locked and endogenous {gamma} - power while increasing RT. While both tACS protocols seem to revert the relationship reported in [4], we argue that tACS produces a shift in attentional resources within visual cortex while leaving unaltered the resources required to conduct the task. This theory is supported by the fact that the correlation between fast RT and high {gamma}- power trials is maintained for tACS sessions too. Finally, we measured cortical excitability by analyzing Event - Related - Potentials (ERP) Lempel - Ziv - Welch Complexity (LZW). In control sessions we observe that lower {gamma} - LZW complexity correlates to faster reaction times. Both metrics are altered by tACS stimulation, as tACS 10 decreased amplitude of the P300 peak, while increasing {gamma}- LZW complexity. To this end, our study highlights the nonlinear cross - frequency interaction between exogenous stimulation and endogenous brain dynamics, and proposes the use of complexity metrics, as LZW, to characterize excitability patterns of cortical areas in a behaviorally relevant timescale. These insights will hopefully contribute to the design of adaptive and personalized tACS protocols where cortical excitability can be characterized through complexity metrics.\n\nAdditional Title Page FootnotesO_LIWe introduce a bursting tACS protocol to study semi-concurrent tACS effects in the visual system and their impact on behavior as measured by reaction time.\nC_LIO_LIBurst 10 Hz tACS (tACS10) applied to the visual cortex entrained {gamma}-oscillations and increased RTs in a change-of-speed detection visual task more than 70 Hz tACS (tACS70) or Control conditions.\nC_LIO_LIBurst tACS10 also decreased amplitude of the P300 peak, while increasing -power and {gamma}-LZW complexity.\nC_LIO_LIPhysiological and behavioral impact of occipital tACS10 and tACS70 was frequency-specific. tACS70 reduced {gamma}-oscillations after 20min of tACS stimulation.\nC_LIO_LICognitive task may determine cortical excitation levels as measured by complexity metrics, as lower {gamma}-LZW complexity correlates to faster reaction times.\nC_LI

neuroscience↗

bioRxiv2017

Insights into regeneration from the genome, transcriptome and metagenome analysis of Eisenia fetida

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. The terrestrial annelids, in spite of their ecological relevance and unique biochemical repertoire, are represented by a single rough genome draft of Eisenia fetida (North American isolate), which suggested that extensive duplications have led to a large number of HOX genes in this annelid. Herein, we report the draft genome sequence of Eisenia fetida (Indian isolate), a terrestrial redworm widely used for vermicomposting assembled using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm, showed that many miRNA gene families have also undergone extensive duplications. Genes for several important proteins such as sialidases and neurotrophins were identified by RNA sequencing of tissue samples. We also used de novo assembled RNA-Seq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue. Sox4, a master regulator of TGF-beta induced epithelial-mesenchymal transition was induced in the newly regenerated tissue. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. The metagenome of the worm, characterized using 16S rRNA sequencing, revealed the identity of several bacterial species that reside in the nephridia of the worm. Comparison of the bodywall and cocoon metagenomes showed exclusion of hereditary symbionts in the regenerated tissue. In summary, we present extensive genome, transcriptome and metagenome data to establish the transcriptome and metagenome dynamics during regeneration.

genomics↗

bioRxiv2017

Intragenomic Redistribution Of Host Transcription Factor Binding With Toxoplasma gondii Infection

The intracellular pathogen Toxoplasma gondii modifies a number of host cell processes. The mechanisms by which T. gondii alters host gene expression are incompletely understood. This study focuses on how the regulators of gene expression in human host cells respond to T. gondii 24 hours following infection to cause specific patterns of transcriptional dysregulation. The most striking finding was the altered landscape of transposase-accessible chromatin by infection. We found both gains and losses of loci of open chromatin enriched in proximity to transcriptionally altered genes. Both DNA sequence motif analysis at the loci changing chromatin accessibility and network analysis of the genes with transcription and regulatory changes implicate a central role for the AP-1 transcription factor. We validated the redistribution of AP-1 in the host genome using chromatin immunoprecipitation studies of the c-Fos component of AP-1. As infection with T. gondii is associated with the cell failing to progress through the cell cycle, all of the changes observed occur in the absence of cell division and within 24 hours, an insight into the dynamism of these transcriptional regulatory events. We conclude that T. gondii infection influences transcriptional regulation through transcription factor re-targeting to modify the cis-regulatory landscape of the host nucleus.\n\nAUTHOR SUMMARYThe complex interactions between the intracellular pathogen Toxoplasma gondii and the host cell manifest as expression changes of host genes. T. gondiis secreted effectors have been extensively studied and include factors that influence the properties of transcription factors, resulting in post-translational modifications and changes in intracellular localization. To gain insights into how T. gondii exerts specific influences on host transcriptional regulation, we used genome-wide approaches to study gene expression, cytosine modifications, and chromatin structure of the host cell 24 hours after infection. The greatest insights were gained from the mapping of loci of transposase-accessible chromatin, revealing a consistently altered pattern of a subset of loci becoming inaccessible, with the simultaneous acquisition of a new set of infection-associated loci of open chromatin. The sequences at these loci were enriched for certain transcription factor binding motifs, in particular that of AP-1, the transcription factor formed by c-Jun and c-Fos heterodimers. Network analysis revealed a central role for c-Jun and c-Fos in the infection-associated perturbations, prompting a chromatin immunoprecipitation approach that confirmed the redistribution of c-Fos in infected cells. We conclude that a T. gondii infection leads to an intragenomic redistribution of host transcription factor binding, with resulting effects on host gene expression.

genomics↗

bioRxiv2017

A simulation study investigating power estimates in Phenome-Wide Association Studies

BackgroundPhenome-wide association studies (PheWAS) are a high-throughput approach to evaluate comprehensive associations between genetic variants and a wide range of phenotypic measures. PheWAS has varying sample sizes for quantitative traits, and variable numbers of cases and controls for binary traits across the many phenotypes of interest, which can affect the statistical power to detect associations. The motivation of this study is to investigate the various parameters which affect the estimation of statistical power in PheWAS, including sample size, case-control ratio, minor allele frequency, and disease penetrance.\n\nResultsWe performed a PheWAS simulation study, where we investigated variations in statistical power based on different parameters, such as overall sample size, number of cases, case-control ratio, minor allele frequency, and disease penetrance. The simulation was performed on both binary and quantitative phenotypic measures. Our simulation on binary traits suggests that the number of cases has more impact than the case to control ratio; also, we found that a sample size of 200 cases or more maintains the statistical power to identify associations for common variants. For quantitative traits, a sample size of 1000 or more individuals performed best in the power calculations. We focused on common genetic variants (MAF>0.01) in this study; however, in future studies, we will be extending this effort to perform similar simulations on rare variants.\n\nConclusionsThis study provides a series of PheWAS simulation analyses that can be used to estimate statistical power for some potential scenarios. These results can be used to provide guidelines for appropriate study design for future PheWAS analyses.

genomics↗

bioRxiv2016

Statistical and biological uncertainties associated with vaccine efficacy estimates and their implications for dengue vaccine impact projections

Given the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia(R) from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) \"statistical uncertainty\" about the numerical value of the vaccines efficacy against disease, and (2) \"biological uncertainty\" about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia(R) took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccines public health impact.

epidemiology↗